Results for "aligned"
Blogs
BBTools for bioinformatician !
...slightly different to prevent collisions. In each case you can see all the possible flags by running the shellscript with no arguments. To bin aligned reads Code: $ p...2287 days ago
Bookmarks
- ...tically-based variant detection tools:* SAMtools: Mpileup* GATK: Unified Genotyper* FreeBayesEach of these tools takes as its input a BAM file of aligned reads and generates a list of...
3669 days ago
- ...on among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilo...
3025 days ago
- +26 more Bookmarks
Pages
Genome Assembly Tools and Software - PART2 !!
...or Accurate Haplotype AssemblyHapCompass for polyploid genomes can currently be used to create accurate pairwise SNP phasings.Given a set of aligned sequence reads in a SAM file...2702 days ago
Awesome perl frameworks, libraries and software - PART 3
...tration hokaccha/nodebrew - Node.js version manager pasky/speedread - A simple terminal-based open source Spritz-alike (per-word RSVP aligned on optimal reading points) p...2511 days ago
Top-level pages
Next generation sequencing in R or bioconductor environment
...Motif Discovery cosmo The cosmo package allows to search a set of unaligned DNA sequences for a shared mo...blication ] PICS The PICS package applies probabilistic inference to aligned-read ChIP-Seq data in order t...3641 days ago
Commercial and public next-gen-seq (NGS) software
...iversity. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model...3535 days ago
- +5 more Top-level pages
News
- ...ters for read list, genome browser enabled with UMI-specific features and filters, UMI-aware variant calling parameters, and exporting UMI-tagged aligned samples. These all features t...
2388 days ago
Opportunity posts
- ...Assessing the quality of data and filtering of raw reads. 3. Assembling the raw reads-de novo as well as reference mapping. 4. Compression of aligned reads using Jam tools 5. RNA...
3659 days ago
Bio-Scripts
Mapping with BWA-mem or BWA-sampe in one go with python script !
...pping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in paired read mode. BESST pr...2140 days ago
- ...ters based on alignments Filters are active when alignment data are present --aligned Dump only aligned sequences --unaligned...
2143 days ago
- +4 more Bio-Scripts
Tags
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its use as simple as possible without loosing the func...Tags: Gblocks, eliminates, poorly, aligned, positions, divergent, regions, DNA, protein, alignment
2181 days ago
Comments
- ...rol and analysis of high-throughput sequence data. HTSeq HTSeq.The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF fil...
2154 days ago
